#ifndef __ALGORITHM_CIFTI_PARCELLATE_H__
#define __ALGORITHM_CIFTI_PARCELLATE_H__

/*LICENSE_START*/
/*
 *  Copyright (C) 2014  Washington University School of Medicine
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License along
 *  with this program; if not, write to the Free Software Foundation, Inc.,
 *  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 */
/*LICENSE_END*/

#include "AbstractAlgorithm.h"
#include "CiftiBrainModelsMap.h"
#include "CiftiParcelsMap.h"
#include "ReductionEnum.h"
#include <vector>

namespace caret {
    
    class AlgorithmCiftiParcellate : public AbstractAlgorithm
    {
        AlgorithmCiftiParcellate();
    protected:
        static float getSubAlgorithmWeight();
        static float getAlgorithmInternalWeight();
    public:
        AlgorithmCiftiParcellate(ProgressObject* myProgObj, const CiftiFile* myCiftiIn, const CiftiFile* myCiftiLabel, const int& direction, CiftiFile* myCiftiOut,
                                 const ReductionEnum::Enum& method = ReductionEnum::MEAN,
                                 const float& excludeLow = -1.0f, const float& excludeHigh = -1.0f, const bool& onlyNumeric = false,
                                 const bool& legacyMode = false, const float& emptyFillVal = 0.0f, CiftiFile* emptyMaskOut = NULL);
        AlgorithmCiftiParcellate(ProgressObject* myProgObj, const CiftiFile* myCiftiIn, const CiftiFile* myCiftiLabel, const int& direction, CiftiFile* myCiftiOut,
                                 const MetricFile* leftWeights, const MetricFile* rightWeights = NULL, const MetricFile* cerebWeights = NULL,
                                 const ReductionEnum::Enum& method = ReductionEnum::MEAN,
                                 const float& excludeLow = -1.0f, const float& excludeHigh = -1.0f, const bool& onlyNumeric = false,
                                 const bool& legacyMode = false, const float& emptyFillVal = 0.0f, CiftiFile* emptyMaskOut = NULL);
        AlgorithmCiftiParcellate(ProgressObject* myProgObj, const CiftiFile* myCiftiIn, const CiftiFile* myCiftiLabel, const int& direction, CiftiFile* myCiftiOut,
                                 const CiftiFile* ciftiWeights, const ReductionEnum::Enum& method = ReductionEnum::MEAN,
                                 const float& excludeLow = -1.0f, const float& excludeHigh = -1.0f, const bool& onlyNumeric = false,
                                 const bool& legacyMode = false, const float& emptyFillVal = 0.0f, CiftiFile* emptyMaskOut = NULL);
        static CiftiParcelsMap parcellateMapping(const CiftiFile* myCiftiLabel, const CiftiBrainModelsMap& toParcellate, std::vector<int>& indexToParcelOut, const bool& legacyMode = false);
        static OperationParameters* getParameters();
        static void useParameters(OperationParameters* myParams, ProgressObject* myProgObj);
        static AString getCommandSwitch();
        static AString getShortDescription();
    };

    typedef TemplateAutoOperation<AlgorithmCiftiParcellate> AutoAlgorithmCiftiParcellate;

}

#endif //__ALGORITHM_CIFTI_PARCELLATE_H__
